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moose 3.0

MOOSE is the Multiscale Object-Oriented Simulation Environment. It is the base and numerical core for large, detailed simulations including Computational Neuroscience and Systems Biology.

# MOOSE

MOOSE is the Multiscale Object-Oriented Simulation Environment. It is the
core of a modern software platform for the simulation of neural
systems ranging from subcellular components and biochemical reactions
to complex models of single neurons, large networks, and systems-level
processes.


# LICENSE

MOOSE is released under GPLv3.


# HOMEPAGE

http://moose.ncbs.res.in/


# SOURCE REPOSITORY

https://sourceforge.net/projects/moose/


# REQUIREMENTS

## Core MOOSE

- g++ (>= 4.6.x) REQUIRED
--------------
For building the C++ MOOSE core.

- GSL (1.16.x) OPTIONAL
----------------
For core moose numerical computation

- OpenMPI (1.8.x) OPTIONAL
---------------
For running moose in parallel on clusters


## PyMOOSE OPTIONAL

Python interface for core MOOSE API

- Python2 ( >= 2.7.x) REQUIRED
-------------------------
For building the MOOSE Python bindings

- Python-dev ( >= 2.7.x) REQUIRED
-------------------------
Python development headers and libraries

- NumPy ( >= 1.6.x) REQUIRED
-------------------------
For numerical computation in PyMOOSE

- H5py (2.3.x) REQUIRED
---------------------
For reading and writing data to HDF5 files


### Chemical Kinetics Network Simulations OPTIONAL

- GSL (1.16.x) REQUIRED
----------------
For core moose numerical computation

- PyQt4 (4.8.x) REQUIRED
---------------------
For Python GUI

- Matplotlib ( >= 1.1.x) REQUIRED
-------------------------
For plotting simulation results

- SBML (5.9.x) OPTIONAL
---------------------
For reading and writing signalling models to SBML files



### Compartmental Model Viusalization OPTIONAL
- GSL (1.16.x) REQUIRED
----------------
For core moose numerical computation

- OSG (3.2.x) REQUIRED
---------------------
For 3D rendering and simulation of neuronal models

- Qt4 (4.8.x) REQUIRED
---------------------
For C++ GUI of Moogli

- PyQt4 (4.8.x) REQUIRED
---------------------
For Python GUI

- Matplotlib ( >= 1.1.x) REQUIRED
-------------------------
For plotting simulation results


# AUTHORS

- Upinder S. Bhalla - Primary Architect, Chemical kinetic solvers
- Niraj Dudani - Neuronal solver
- Subhasis Ray - PyMOOSE Design and Documentation, Python Plugin Interface, NSDF Format
- G.V.HarshaRani - Web page design, SBML support, Kinetikit Plugin Development
- Aditya Gilra - NeuroML reader development
- Aviral Goel - Moogli/Neurokit Development
- Dilawar Singh - Packaging


# Support:

You can join the MOOSE generic mailing list for your queries -
https://lists.sourceforge.net/lists/listinfo/moose-generic


# Bugs:

You can file bug reports and feature requets at the sourceforge tracker -
http://sourceforge.net/p/moose/bugs/

# Getting started:

MOOSE can be used as a python module. Look into the Demos directory
for sample code. A starting point can be Demos/snippets with useful
python code snippets that can be used as building blocks.

MOOSE also comes with a NeuroML reader. Demos/neuroml has some
python scripts showing how to load NeuroML models.

MOOSE is backward compatible with GENESIS
kinetikit. Demos/Genesis_files has some examples. You can load a
kinetikit model with the loadModel function:

moose.loadModel(kkit_file_path, target_model_path)

You can also load GENESIS prototype files. The same loadModel
function can be used for this (but you need to have all the channels
used in the prototype preloaded in /library):

moose.loadModel(prototype_file_path, prototype_model_path)

Top level moose documentation can be accessed in the Python
interpreter the usual way:

import moose
help(moose)


MOOSE classes have built-in documentation that can be accessed via
the `doc()` function -

moose.doc(classname)

This will give the full documentation for the class including the fields
available.

`moose.doc(classname.fieldname)`
will give you information about a particular field in a class.

Complete MOOSE Documentation can be found at -
http://moose.ncbs.res.in/content/view/5/6/  
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moose-3.0.tar.gz (md5) Source 2014-08-03 4MB
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